X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=django_simple%2Ftodo%2Fjobfiles.py;h=e7ee71653117be5f5c45c3b04e8f73c76ba09a13;hb=56595cc7938f5c7b53dd3ebe91b2a42f52cb89d1;hp=69c809edd75e8c192e20fc974e4ebfbc8ded08e1;hpb=591ac48194b207c02ffd7cda59c1c9709a114498;p=django_unres.git diff --git a/django_simple/todo/jobfiles.py b/django_simple/todo/jobfiles.py index 69c809e..e7ee716 100644 --- a/django_simple/todo/jobfiles.py +++ b/django_simple/todo/jobfiles.py @@ -13,26 +13,69 @@ import textwrap logging.basicConfig() logger = logging.getLogger(__name__) +def seq_2d_xx(line,seq): + line=line.replace(" ","") + lista=list(line) + for ii in range(0,len(line)): + if seq[ii]=='X': + if ii>0: + lista[ii-1]='-' + if ii+10: + if len(list)>0: return str(len(list))+' '+' '.join(map(str,list_sorted))+'\n'+\ str(len(ssbond))+' '+' '.join(map(str,list))+'\n' - else: + else: return '0\n' @receiver(post_save, sender=Task) def write_on_task_save(sender, instance, **kwargs): - if instance.ready and not instance.done and instance.running==0: + if instance.ready and not instance.done and instance.running==0 and instance.pbsjob=='': if (not os.path.isdir(instance.jobdirname)): os.mkdir(instance.jobdirname) - os.chdir(instance.jobdirname) +# os.chdir(instance.jobdirname) @@ -41,21 +84,37 @@ def write_on_task_save(sender, instance, **kwargs): #wrapper = textwrap.TextWrapper(width=70) #word_list = wrapper.wrap(text=md.substitute(nstep=str(nstep))) - w="""WSC=1.00000 WSCP=1.23315 WELEC=0.84476 WBOND=1.00000 WANG=0.62954 & + if instance.unres_ff =='FF2': + w="""WSC=1.00000 WSCP=1.23315 WELEC=0.84476 WBOND=1.00000 WANG=0.62954 & WSCLOC=0.10554 WTOR=1.34316 WTORD=1.26571 WCORRH=0.19212 WCORR5=0.00000 & WCORR6=0.00000 WEL_LOC=0.37357 WTURN3=1.40323 WTURN4=0.64673 WTURN6=0.00000 & WVDWPP=0.23173 WHPB=1.00000 WSCCOR=0.25 & -CUTOFF=7.00000 WCORR4=0.00000 -""" +CUTOFF=7.00000 WCORR4=0.00000""" + elif instance.unres_ff =='NEWCT-9P': + w="""WSC=0.81230 WSCP=1.20420 WELEC=0.87690 WBOND=1.00000 WANG=1.97730 & +WSCLOC=0.063657 WTOR=1.41540 WTORD=0.00000 WCORRH=0.00000 WCORR5=0.00000 & +WCORR6=0.00000 WEL_LOC=0.036638 WTURN3=1.45110 WTURN4=0.00000 WTURN6=0.00000 & +WSCCOR=0.00000 WVDWPP=0.33393 WHPB=1.00000 WSCP14=0.00000 & +CUTOFF=7.00000 WCORR4=0.00000""" + else: + w="""WSC=0.82686 WSCP=0.96947 WELEC=0.79373 WBOND=1.00000 WANG=0.46542 & +WSCLOC=0.07969 WTOR=0.81684 WTORD=0.67806 WCORRH=0.00000 WCORR5=0.00000 & +WCORR6=0.00000 WEL_LOC=0.71100 WTURN3=2.30298 WTURN4=0.86517 WTURN6=0.00000 & +WSCCOR=0.14577 WVDWPP=0.17781 WHPB=1.00000 WSCP14=0.00000 & +CUTOFF=7.00000 WCORR4=0.00000""" + - with open('file.inp','w') as f: + with open(instance.jobdirname+'/file.inp','w') as f: f.write(instance.name + ' UNRES server job'+ '\n') if instance.type == 'min' : control_line = 'SEED='+str(instance.md_seed)+' ' \ + instance.min_choice \ - + ' pdbstart pdbref BOXX=1000. BOXY=1000. BOXZ=1000. ' + + ' pdbstart pdbref ' \ + + ' BOXX='+str(instance.boxx) \ + + ' BOXY='+str(instance.boxy) \ + + ' BOXZ='+str(instance.boxz) +' ' if not instance.min_overlap: control_line = control_line+'overlap ' if not instance.min_searchsc: @@ -64,6 +123,8 @@ CUTOFF=7.00000 WCORR4=0.00000 control_line = control_line+'pdbout ' if instance.min_unres_pdb: control_line = control_line+'unres_pdb ' + if instance.unres_ff =='NEWCT-9P': + control_line = control_line+'tormode=2 ' type_line = 'print_min_ini print_min_res print_min_stat'\ +' MAXMIN='+str(instance.min_maxmin)\ @@ -78,7 +139,7 @@ CUTOFF=7.00000 WCORR4=0.00000 if seq[-1]=='X': dimen3-=1 - nogly ='CDSQKIPTFNHLRWAVEYM' + nogly ='CDSQKIPTFNHLRWAVEYMcdsqkiptfnhlrwaveym' seq2 = ''.join([c for c in seq if c in nogly]) dimen3=(dimen3+len(seq2))*3 @@ -86,11 +147,18 @@ CUTOFF=7.00000 WCORR4=0.00000 if instance.type == 'md' : control_line = 'SEED='+str(instance.md_seed)+' '\ - +instance.md_start +' md one_letter BOXX=1000. BOXY=1000. BOXZ=1000. ' + +instance.md_start +' md one_letter'\ + + ' BOXX='+str(instance.boxx) \ + + ' BOXY='+str(instance.boxy) \ + + ' BOXZ='+str(instance.boxz) +' ' + if instance.md_pdbref: control_line = control_line+'pdbref ' + + if instance.unres_ff =='NEWCT-9P': + control_line = control_line+'tormode=2 cart' - type_line = 'reset_vel=0'\ + type_line = ' reset_vel=0'\ +' t_bath='+str(instance.md_temp)\ +' nstep='+str(instance.md_nstep)\ +' ntwe='+str(instance.md_ntwe)\ @@ -107,17 +175,36 @@ CUTOFF=7.00000 WCORR4=0.00000 if instance.md_mdpdb: type_line = type_line + ' mdpdb ' - if instance.type == 'remd' : + if instance.type == 'remd' or instance.type == 'dock': control_line = 'SEED='+str(instance.md_seed)+' '\ - +instance.md_start +' re one_letter BOXX=1000. BOXY=1000. BOXZ=1000. ' + +instance.md_start +' re one_letter'\ + + ' BOXX='+str(instance.boxx) \ + + ' BOXY='+str(instance.boxy) \ + + ' BOXZ='+str(instance.boxz) +' ' + + if instance.type == 'dock': + control_line = control_line+'CONSTR_HOMOL=24 ' + if instance.md_pdbref: control_line = control_line+'pdbref ' - + + if instance.unres_ff =='NEWCT-9P': + control_line = control_line+'tormode=2 cart' + + cntrl_saxs='' + if instance.saxs_data != '': + lines=instance.saxs_data.split('\n') + nsaxs=0 + for line in lines: + if len(line.split())==2: + nsaxs+=1 + cntrl_saxs=' nsaxs='+str(nsaxs)+' scal_rad='+str(instance.scal_rad) + control_line += cntrl_saxs - type_line = 'reset_vel='+ str(instance.remd_nstex)\ + type_line = ' reset_vel='+ str(instance.remd_nstex)\ +' nstep='+str(instance.md_nstep)\ +' ntwe='+str(instance.md_ntwe)\ - +' ntwx='+str(instance.remd_nstex)\ + +' ntwx='+str(instance.md_ntwx)\ +' dt='+str(instance.md_dt) if instance.md_lang == 'langevin': type_line = type_line + ' lang=1 ' @@ -127,13 +214,13 @@ CUTOFF=7.00000 WCORR4=0.00000 type_line = type_line + 'tau_bath='+str(instance.md_tau) if instance.md_respa: type_line = type_line + ' respa ' - if instance.md_mdpdb: - type_line = type_line + ' mdpdb ' +# if instance.md_mdpdb: +# type_line = type_line + ' mdpdb ' type_line2 = 'nrep='+str(instance.remd_nrep) \ +' nstex='+str(instance.remd_nstex) \ +' tlist mlist sync nsyn='+str(instance.remd_nstex)\ - +' traj1file rest1file ' + +' traj1file rest1file TRAJCACHE=200' if instance.md_start == 'pdbstart': type_line = type_line + ' preminim cart' @@ -150,11 +237,15 @@ CUTOFF=7.00000 WCORR4=0.00000 f.write('{:79}'.format(element)+'&\n') f.write(word_list[-1]+'\n') - if instance.md_start == 'pdbstart': + if instance.md_start == 'pdbstart' and instance.unres_ff !='NEWCT-9P': + if instance.type == 'remd' or instance.type == 'dock': + f.write('print_min_ini print_min_res print_min_stat maxfun='+ + str(instance.min_maxfun)+'\n') + else: f.write('print_min_ini print_min_res print_min_stat\n') - if instance.type == 'remd' : + if instance.type == 'remd' or instance.type == 'dock': word_list = wrapper.wrap(text=type_line2) for element in word_list[:-1]: f.write('{:79}'.format(element)+'&\n') @@ -173,15 +264,33 @@ CUTOFF=7.00000 WCORR4=0.00000 for element in word_list[:-1]: f.write('{:79}'.format(element)+'&\n') f.write(word_list[-1]+'\n') - - f.write(w) + + if instance.saxs_data != '': + w+=' wsaxs='+str(instance.wsaxs) + f.write(w+'\n') if instance.type == 'min' or instance.md_start == 'pdbstart': - f.write('plik.pdb\n') + if instance.type == 'dock': + f.write('plik1ter.pdb\n') + else: + f.write('plik.pdb\n') f.write(write_ssbond(instance.ssbond)) - f.write('0\n') - + if instance.md_2d == '': + f.write('0\n') + else: + if instance.unres_ff =='NEWCT-9P': + f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq))) + else: + f.write(seq_2d_write(seq_2d_xx(instance.md_2d,seq))) + + if instance.type == 'dock': + f.write('HOMOL_DIST=0.1 HOMOL_ANGLE=1.0 HOMOL_THETA=1.0 HOMOL_SCD=1.0 DIST_CUT=15.0 &\n') + f.write('READ2SIGMA START_FROM_MODELS\n') + for i in range(1,10): + f.write('model0'+str(i)+'.pdb\n') + for i in range(10,25): + f.write('model'+str(i)+'.pdb\n') if instance.type == 'md' and instance.md_start != 'pdbstart': @@ -190,7 +299,15 @@ CUTOFF=7.00000 WCORR4=0.00000 f.write(str(len(seq))+'\n') for i in range(0,len(seq),80): f.write(seq[i:i+80]+'\n') - f.write('0\n0\n') + f.write('0\n') + if instance.md_2d == '': + f.write('0\n') + else: + if instance.unres_ff =='NEWCT-9P': + f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq))) + else: + f.write(seq_2d_write(seq_2d_xx(instance.md_2d,seq))) + if instance.type == 'remd' and instance.md_start != 'pdbstart': @@ -199,32 +316,60 @@ CUTOFF=7.00000 WCORR4=0.00000 f.write(str(len(seq))+'\n') for i in range(0,len(seq),80): f.write(seq[i:i+80]+'\n') - f.write('0\n0\n') - - + f.write('0\n') + if instance.md_2d == '': + f.write('0\n') + else: + if instance.unres_ff =='NEWCT-9P': + f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq))) + else: + f.write(seq_2d_write(seq_2d_xx(instance.md_2d,seq))) + + + if instance.saxs_data != '': + lines=instance.saxs_data.split('\n') + for line in lines: + tmp=line.split() + if len(tmp)==2: + f.write(tmp[0]+' '+tmp[1]+'\n') if instance.type == 'min': - shutil.copy('../files/pbs.csh','.') + os.chdir(instance.jobdirname) + if instance.unres_ff =='FF2': + shutil.copy('../files/pbs.csh','.') + elif instance.unres_ff =='NEWCT-9P': + shutil.copy('../files/pbs_newct-9p.csh','pbs.csh') + else: + shutil.copy('../files/pbs_new.csh','pbs.csh') ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT) + os.chdir('..') elif instance.type == 'md': - f1 = open('../files/pbs_md.csh', 'r') + os.chdir(instance.jobdirname) + if instance.unres_ff =='FF2': + f1 = open('../files/pbs_md.csh', 'r') + elif instance.unres_ff =='NEWCT-9P': + f1 = open('../files/pbs_md_newct-9p.csh', 'r') + else: + f1 = open('../files/pbs_md_new.csh', 'r') f2 = open('pbs.csh', 'w') for line in f1: - f2.write(line.replace('$dimen3',str(dimen3) )) + f2.write(line.replace('$dimen3',str(dimen3)+' '+str(instance.md_temp) )) f1.close() f2.close() f1 = open('file.seq', 'w') for i in range(0,len(seq),80): f1.write(seq[i:i+80]+'\n') + f1.write('\n') f1.close() ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT) + os.chdir('..') else: +# instance.type == 'remd' tmp1=json.loads(instance.remd_multi_m) nreplicas=sum(map(int, tmp1)) - # hardcoded for 4 core nodes with FGPROC=2 nodes=int(nreplicas*2/4) reszta = nreplicas*2-nodes*4 @@ -232,74 +377,196 @@ CUTOFF=7.00000 WCORR4=0.00000 pbs = '#PBS -l nodes='+str(nodes)+':ppn=4' else: pbs = '#PBS -l nodes='+str(nodes)+':ppn=4+1:ppn='+str(reszta) - - f1 = open('../files/pbs8.csh', 'r') + + tmp_ss='' + if instance.ssbond!='': + ix=[] + ii=0 + for i in range(0,len(seq)): + if seq[i]=='X': + ii=ii+1 + ix.append(ii) + l=[] + ss=json.loads(instance.ssbond) + for e in ss: + l.append(e[0]-ix[e[0]]) + l.append(e[1]-ix[e[1]]) + tmp_ss=' '.join(map(str,l)) + + os.chdir(instance.jobdirname) + if instance.unres_ff =='FF2': + f1 = open('../files/pbs8.csh', 'r') + elif instance.unres_ff =='NEWCT-9P': + f1 = open('../files/pbs8_newct-9p.csh', 'r') + else: + f1 = open('../files/pbs8_new.csh', 'r') f2 = open('pbs8.csh', 'w') for line in f1: if '#PBS -l nodes=4:ppn=4' in line: f2.write(line.replace('#PBS -l nodes=4:ppn=4', pbs)) + elif '$ssbond' in line: + f2.write(line.replace('$ssbond',tmp_ss)) + elif 'cd $PBS_O_WORKDIR' in line and instance.type == 'dock': + f2.write(line) + if instance.dock_peptide: + f2.write('../files/generator_v13 plik.pdb plik2.pdb 1 \n') + else: + f2.write('../files/generator_v13 plik.pdb plik2.pdb 0 \n') + f2.write("sed '/END/q' plik.pdb |grep ATOM > plik1ter.pdb \n") + f2.write("echo TER >> plik1ter.pdb \n") + f2.write("sed '/END/q' plik2.pdb |grep ATOM >> plik1ter.pdb \n") else: tmp1=json.loads(instance.remd_multi_t) - f2.write(line.replace('$temperatures','"'+" ".join(tmp1)+'"')) + f2.write(line.replace('$temperatures','"'+" ".join(tmp1)+'" '+str(nreplicas))) f1.close() - f2.close() + f2.close() + + f1 = open('file.seq', 'w') + for i in range(0,len(seq),80): + f1.write(seq[i:i+80]+'\n') + f1.write('\n') + f1.close() + + os.chdir('..') # write wham & cluster input - with open('file_wham.inp','w') as f: - if instance.md_nstep/instance.remd_nstex*nreplicas<=8000: + with open(instance.jobdirname+'/file_wham.inp','w') as f: + if instance.md_nstep/instance.md_ntwx*nreplicas<=8000: isampl=1 else: - isampl=int(instance.md_nstep/instance.remd_nstex*nreplicas/8000) - + isampl=int(instance.md_nstep/instance.md_ntwx*nreplicas/8000) + f.write('{:79}'.format(' isampl='+str(isampl))+'&\n') if instance.md_pdbref: - f.write('SEED='+str(instance.md_seed)+' isampl='+str(isampl)+ - ' einicheck=1 rescale=2 delta=0.02 cxfile classify\n') + f.write('{:79}'.format('SEED='+str(instance.md_seed)+ + ' einicheck=1 rescale=2 delta=0.02 cxfile classify')+'&\n') else: - f.write('SEED='+str(instance.md_seed)+' isampl='+str(isampl)+ - ' einicheck=1 rescale=2 delta=0.02 cxfile\n') + f.write('{:79}'.format('SEED='+str(instance.md_seed)+ + ' einicheck=1 rescale=2 delta=0.02 cxfile')+'&\n') + if instance.md_2d != '': + f.write('{:79}'.format(' WITH_DIHED_CONSTR')+'&\n') + if instance.type == 'dock': + f.write('{:79}'.format(' n_ene=19 CONSTR_HOMOL=24')+'&\n') + if instance.unres_ff =='NEWCT-9P': + f.write('{:79}'.format('tormode=2 ')+'&\n') + f.write('BOXX='+str(instance.boxx)+' BOXY='+str(instance.boxy)+ + ' BOXZ='+str(instance.boxz)+cntrl_saxs +'\n') + f.write('nres='+str(len(seq))+' one_letter\n') for i in range(0,len(seq),80): f.write(seq[i:i+80]+'\n') f.write(write_ssbond(instance.ssbond)) - - f.write(w) + if instance.type == 'dock': + f.write('HOMOL_DIST=0.1 HOMOL_ANGLE=1.0 HOMOL_THETA=1.0 HOMOL_SCD=1.0 DIST_CUT=15.0 &\n') + f.write('READ2SIGMA \n') + for i in range(1,10): + f.write('model0'+str(i)+'.pdb\n') + for i in range(10,25): + f.write('model'+str(i)+'.pdb\n') + + if instance.md_2d != '': + f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq))) + + if instance.saxs_data != '': + saxs_r=[] + saxs_P=[] + saxs_norm=0 + r_last=None + fsaxs = open(instance.jobdirname+'/saxs.data', 'w') + lines=instance.saxs_data.split('\n') + for line in lines: + tmp=line.split() + if len(tmp)==2: + f.write(tmp[0]+' '+tmp[1]+'\n') + saxs_r.append(tmp[0]) + saxs_P.append(float(tmp[1])) + if r_last==None: + r_last=float(tmp[0]) + else: + saxs_norm += float(tmp[1])*(float(tmp[0])-r_last) + r_last=float(tmp[0]) + for r,p in zip(saxs_r,saxs_P): + fsaxs.write('{} {}\n'.format(r,p/saxs_norm)) + fsaxs.close() + + f.write(w+'\n') f.write('\n') f.write('nt='+str(instance.remd_nrep)+' replica read_iset\n') tmp1=json.loads(instance.remd_multi_t) for element in tmp1: f.write('nr=1 temp='+element+' fi=0.0 0.0 0.0 0.0 0.0\n') f.write('kh= 0.0 Q0=0.0\n') - rec=instance.md_nstep/instance.remd_nstex + rec=instance.md_nstep/instance.md_ntwx f.write('nfile_cx=1 rec_start='+str(rec/10) +' rec_end='+str(rec)+' totraj='+str(nreplicas)+'\n') f.write('file_MD000\n') if instance.md_pdbref: f.write('pdbref\n') - f.write('plik.pdb\n') + if instance.type == 'dock': + f.write('plik1ter.pdb\n') + else: + f.write('plik.pdb\n') - with open('file_cluster.inp','w') as f: + with open(instance.jobdirname+'/file_cluster.inp','w') as f: f.write(instance.name + ' UNRES server job'+ '\n') - f.write('nres='+str(len(seq)) + f.write('{:79}'.format('nres='+str(len(seq)) +' one_letter rescale=2 PRINT_CART PDBOUT=1 iopt=1' - +' temper='+str(instance.remd_cluter_temp)+'\n') - f.write(w) + +' temper='+str(instance.remd_cluter_temp))+'&\n') + if instance.md_2d != '': + f.write('{:79}'.format(' WITH_DIHED_CONSTR')+'&\n') + if instance.type == 'dock': + f.write('{:79}'.format(' CONSTR_HOMOL=24')+'&\n') + if instance.unres_ff =='NEWCT-9P': + f.write('{:79}'.format('tormode=2 ')+'&\n') + f.write('BOXX='+str(instance.boxx)+' BOXY='+str(instance.boxy)+ + ' BOXZ='+str(instance.boxz)+cntrl_saxs +'\n') + f.write(w+'\n') for i in range(0,len(seq),80): f.write(seq[i:i+80]+'\n') f.write(write_ssbond(instance.ssbond)) - + if instance.type == 'dock': + f.write('HOMOL_DIST=0.1 HOMOL_ANGLE=1.0 HOMOL_THETA=1.0 HOMOL_SCD=1.0 DIST_CUT=15.0 &\n') + f.write('READ2SIGMA \n') + for i in range(1,10): + f.write('model0'+str(i)+'.pdb\n') + for i in range(10,25): + f.write('model'+str(i)+'.pdb\n') + if instance.md_2d != '': + f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq))) + if instance.saxs_data != '': + lines=instance.saxs_data.split('\n') + for line in lines: + tmp=line.split() + if len(tmp)==2: + f.write(tmp[0]+' '+tmp[1]+'\n') + + os.chdir(instance.jobdirname) ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs8.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT) + os.chdir('..') + + output = str(ret_code.communicate()[0]) + output=output.strip() + if output=='': + output='error' + logger.warning("PBS \"%s\" " % output) + instance.pbsjob = output + instance.save() - print ret_code.stdout.readlines() - os.chdir('..') +# print ret_code.stdout.readlines() logger.warning("Dir \"%s\" has been saved." % instance.jobdirname) @receiver(post_delete, sender=Task) def delete_on_task_del(sender, instance, **kwargs): if instance.jobdirname: if os.path.isdir(instance.jobdirname): + if not instance.done: + ret_code_qdel = subprocess.Popen(' /opt/torque/bin/qdel '+str(instance.pbsjob), shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT) + output = str(ret_code_qdel.communicate()[0]) + output=output.strip() + logger.warning("PBS qdel \"%s\" " % instance.pbsjob) + logger.warning("QDEL \"%s\" " % output) shutil.rmtree(instance.jobdirname) logger.warning("Dir \"%s\" has been rm." % instance.jobdirname) \ No newline at end of file